H5EBSD Data File Specification¶

DREAM.3D can store EBSD data from multiple vendors in a data file using the HDF5 file format library. Although the general layout of the HDF5 file is the same between vendors, there are details that are not the same between vendors, because each vendor chooses to save different types of data. The top level datasets that deal with the basic volume information is the same for every file.

HDF5 File Layout¶

HDF5 Root Level Layout Specification¶

Root Level Attributes	Type	Name/Comments/Default Value
FileVersion	H5T_NATIVE_INT32	Current Value="5"
EsdLibVersion	H5T_STRING	Optional value that states what version of the library wrote the file

Root Level Data sets	HDF5 Type	Name/Comments/Default Value
Index	An array of all the slice values. As of DREAM3D Version 5 this is not really used but could handy if the list of slices starts to get large.
EulerTransformationAngle	H5T_NATIVE_FLOAT	Degrees
EulerTransformationAxis	H5T_NATIVE_FLOAT	3x1 Array (Example 0,0,1)
Manufacturer	H5T_STRING	The Manufacturer currently is either TSL or HKL
Max X Points	H5T_NATIVE_INT64	The maximum number of X points in the sample grid
Max Y Points	H5T_NATIVE_INT64	The maximum number of Y points in the sample grid
SampleTransformationAngle	H5T_NATIVE_FLOAT	Degrees
SampleTransformationAxis	H5T_NATIVE_FLOAT	3x1 Array (Example 0,0,1)
Stacking Order	H5T_NATIVE_UINT32	Defines which slice corresponds to the Z=0 in the coordinate system. 0=Low to High. 1 = High to Low. Optional Attribute of type H5T_STRING, with Name "Name" and Value ("Low To High" or "High To Low")
X Resolution	H5T_NATIVE_FLOAT	Resolution between sample points in the X direction
Y Resolution	H5T_NATIVE_FLOAT	Resolution between sample points in the Y direction
Z Resolution	H5T_NATIVE_FLOAT	Resolution between slices in the Z Direction
ZEndIndex	H5T_NATIVE_INT64	Starting Slice index
ZStartIndex	H5T_NATIVE_INT64	Ending Slice index (inclusive)
Index	An array of all the slice values. As of DREAM3D Version 5 this is not really used but could handy if the list of slices starts to get large.

Slice Group Specification¶

Each Slice is grouped into its own H5G_GROUP with the Name of the group as the index of the slice. Within each slice group there are two (2) more groups with names Data and Header

Name	HDF5 Type	Value
Data	H5G_GROUP	Contains all the data columns
Header	H5G_GROUP	Contains all the header entries

TSL Specification¶

This section details the data to be imported from a .ang file into the .h5ebsd file.

TSL (.ang) Data Group Specification¶

Name	HDF5 Type	Value
Phi1	H5T_NATIVE_FLOAT	Contains all the Phi1 data in a 1D Array with length equal to the total number of points.
Phi	H5T_NATIVE_FLOAT	Contains all the Phi data in a 1D Array with length equal to the total number of points.
Phi2	H5T_NATIVE_FLOAT	Contains all the Phi2 data in a 1D Array with length equal to the total number of points.
X Position	H5T_NATIVE_FLOAT	Contains all the X position data in a 1D Array with length equal to the total number of points.
Y Position	H5T_NATIVE_FLOAT	Contains all the Y position data in a 1D Array with length equal to the total number of points.
Image Quality	H5T_NATIVE_FLOAT	Contains all the Image Quality data in a 1D Array with length equal to the total number of points.
Confidence Index	H5T_NATIVE_FLOAT	Contains all the Confidence Index data in a 1D Array with length equal to the total number of points.
PhaseData	H5T_NATIVE_INT32	Contains all the PhaseData data in a 1D Array with length equal to the total number of points.
SEM Signal	H5T_NATIVE_FLOAT	Contains all the SEM Signal data in a 1D Array with length equal to the total number of points.
Fit	H5T_NATIVE_FLOAT	Contains all the Fit of Solution data in a 1D Array with length equal to the total number of points.

TSL (.ang) Header Group Specification¶

Name	HDF5 Type	Value
OriginalFile	H5T_STRING	Path to the .ang file that was imported
OriginalHeader	H5T_STRING	Contains the original header from the imported .ctf file
TEM_PIXperUM	H5T_NATIVE_FLOAT	Contains value for the header entry TEM_PIXperUM
x-star	H5T_NATIVE_FLOAT	Contains value for the header entry x-star
y-star	H5T_NATIVE_FLOAT	Contains value for the header entry y-star
z-star	H5T_NATIVE_FLOAT	Contains value for the header entry z-star
WorkingDistance	H5T_NATIVE_FLOAT	Contains value for the header entry WorkingDistance
ElasticConstants	H5T_STRING	Contains value for the header entry ElasticConstants
GRID	H5T_STRING	Contains value for the header entry GRID
XSTEP	H5T_NATIVE_FLOAT	Contains value for the header entry XSTEP
YSTEP	H5T_NATIVE_FLOAT	Contains value for the header entry YSTEP
NCOLS_ODD	H5T_NATIVE_INT32	Contains value for the header entry NCOLS_ODD
NCOLS_EVEN	H5T_NATIVE_INT32	Contains value for the header entry NCOLS_EVEN
NROWS	H5T_NATIVE_INT32	Contains value for the header entry NROWS
OPERATOR	H5T_STRING	Contains value for the header entry OPERATOR
SAMPLEID	H5T_STRING	Contains value for the header entry SAMPLEID
SCANID	H5T_STRING	Contains value for the header entry SCANID
Phases	H5G_GROUP	Group that contains a subgroup for each phase where the name of each subgroup is the index of the phase starting at 1.

TSL (.ang) Phase Group Specification¶

Name	HDF5 Type	Value
Categories	H5T_NATIVE_INT32
Formula	H5T_STRING
Info	H5T_STRING
LatticeConstants	H5T_NATIVE_FLOAT
Material Name	H5T_STRING
NumberFamilies	H5T_NATIVE_INT32
Phase	H5T_NATIVE_INT32
Symmetry	H5T_NATIVE_INT32
hklFamilies	H5G_GROUP	Contains all the HKL Family information where the number of datasets contained in this group is the number of HKL Families

TSL (.ang) HKLFamily Group Specification¶

Name	HDF5 Type	Value
{Based on Index of the family}. If there are 4 families then there are 4 data sets with names "0", "1", "2" and "3".	Custom: See Below

typedef struct
{
    int h;
    int k;
    int l;
    int s1;
    float diffractionIntensity;
    int s2;
} HKLFamily_t;

HKL Specification¶

This section details the data to be imported from a .ctf file into the .h5ebsd file

HKL (.ctf) Data Group Specification¶

1D Array of Values, where the number of elements in the array is equal to the total number of points per 2D Slice.

Name	HDF5 Type	Value
Phase	H5T_NATIVE_INT32
X	H5T_NATIVE_FLOAT
Y	H5T_NATIVE_FLOAT
Z	H5T_NATIVE_FLOAT	Note that this ONLY appears in a "3D" .ctf data file
Bands	H5T_NATIVE_INT32
Error	H5T_NATIVE_INT32
Euler1	H5T_NATIVE_FLOAT	In 2D files these are in Degrees. In 3D files these are in Radians
Euler2	H5T_NATIVE_FLOAT	In 2D files these are in Degrees. In 3D files these are in Radians
Euler3	H5T_NATIVE_FLOAT	In 2D files these are in Degrees. In 3D files these are in Radians
MAD	H5T_NATIVE_FLOAT
BD	H5T_NATIVE_INT32
BS	H5T_NATIVE_INT32
GrainIndex	H5T_NATIVE_INT32
GrainRandomColourR	H5T_NATIVE_UINT8
GrainRandomColourG	H5T_NATIVE_UINT8
GrainRandomColourB	H5T_NATIVE_UINT8

HKL (.ctf) Header Specification¶

Name	HDF5 Type	Value
OriginalFile	H5T_STRING	Path to the .ctf file that was imported
OriginalHeader	H5T_STRING	Contains the original header from the imported .ctf file
Prj	H5T_STRING	Contains value for the header entry Prj
Author	H5T_STRING	Contains value for the header entry Author
JobMode	H5T_STRING	Contains value for the header entry JobMode
XCells	H5T_NATIVE_INT32	Contains value for the header entry XCells
YCells	H5T_NATIVE_INT32	Contains value for the header entry YCells
XStep	H5T_NATIVE_FLOAT	Contains value for the header entry XStep
YStep	H5T_NATIVE_FLOAT	Contains value for the header entry YStep
ZStep	H5T_NATIVE_FLOAT	Contains value for the header entry ZStep
ZCells	H5T_NATIVE_FLOAT	Contains value for the header entry ZCells
AcqE1	H5T_NATIVE_FLOAT	Contains value for the header entry AcqE1
AcqE2	H5T_NATIVE_FLOAT	Contains value for the header entry AcqE2
AcqE3	H5T_NATIVE_FLOAT	Contains value for the header entry AcqE3
Mag	H5T_NATIVE_INT32	Contains value for the header entry Mag
Coverage	H5T_NATIVE_INT32	Contains value for the header entry Coverage
Device	H5T_NATIVE_INT32	Contains value for the header entry Device
KV	H5T_NATIVE_INT32	Contains value for the header entry KV
TiltAngle	H5T_NATIVE_FLOAT	Contains value for the header entry TiltAngle
TiltAxis	H5T_NATIVE_FLOAT	Contains value for the header entry TiltAxis
Phases	H5G_GROUP	Group that contains a subgroup for each phase where the name of each subgroup is the index of the phase starting at 1.

HKL (.ctf) Phase Group Specification¶

Name	HDF5 Type	Value
Comment	H5T_STRING	Contains value for the header entry Comment
Internal1	H5T_STRING	Contains value for the header entry Internal1
Internal2	H5T_STRING	Contains value for the header entry Internal2
LatticeAngles	H5T_NATIVE_FLOAT	Contains value for the header entry Lattice Angles in a 1x3 array
LatticeDimensions	H5T_NATIVE_FLOAT	Contains value for the header entry Lattice Dimensions in a 1x3 array
LaueGroup	H5T_NATIVE_INT32	Contains value for the header entry LaueGroup plus an H5T_STRING Attribute which is the string name of the Laue Group, for example "Hexagonal-High 6/mmm"
SpaceGroup	H5T_NATIVE_INT32	Contains value for the header entry SpaceGroup
PhaseName	H5T_STRING	Contains value for the header entry PhaseName

Stacking Order Discussion¶

The stacking order refers to the order in which the z slices are stacked together when they are read from the file. The enumerations are also in the EbsdLibConstants.h header file.

As a further explanation, if the ordering is Low To High, then the slice with the lowest number is positioned at Z=0 in 3D Cartesian space. For example, if your data set is numbered from 23 to 86 with file names of the form Slice_023.ang and you select "Low To High", then the data inside of file Slice_023.ang will be positioned at Z=0 during any method that has to deal with the data. The opposite of this is if the user were to select to have their data High to Low, in which case, the file with name Slice_086.ang will be positioned at Z=0 and the file with name "Slice_023.ang" will be positioned at Z=64.